Publication short list

Bandyopadhyay S, Mehta M, Kuo D, Sung MK, Chuang R, Jaehnig EJ, Bodenmiller D, Licon K, Copeland W, Shales M, Fiedler D, Dutkowski J, Guenole A, van Attikum H, Shokat KM, Kolodner RD, Huh WK, Aebersold R, Keogh MC, Krogan NJ, Ideker T. Rewiring of genetic networks in response to DNA damage. Science 330:1385-1389 (2010) [Get PDF] [Suppl Docs] [Pubmed link]
Ravasi, T., Suzuki, H., Cannistraci, C.V., et al. An atlas of combinatorial transcriptional regulation in mouse and man. Cell 14 (5):744-752 (2010) [Get PDF] [Pubmed link]
Roguev, A., Bandyopadhyay, S., Zofall, M., Zhang, K., Fischer, T., Collins, S.R., Qu, H., Shales, M., Park, H.O., Hayles, J., Hoe, K.L., Kim, D.U., Ideker, T.*, Grewal, S.I.*, Weissman, J.S.*, Krogan, N.J.* Conservation and rewiring of functional modules revealed by an epistasis map in fission yeast. Science. 322:405-410 (2008). [Get PDF] [Pubmed link]
*Corresponding Authors
Ideker T. Forging new ties between E. coli genes. Cell. 133:1135-1137 (2008). [Get PDF] [Pubmed link]
Chuang, HY, Lee, E, Liu, YT, Lee, D, and Ideker, T. Network-based classification of breast cancer metastasis. Mol Syst Biol. 3:140 (2007). [Get PDF] [Online link]
Workman, CT., Mak, HC., McCuine, S., Tagne, JB., Agarwal, M., Ozier, O., Begley, TJ., Samson, LD., Ideker, T. A Systems Approach to Mapping DNA Damage Response Pathways. Science. 312 (5776):1054-1059 (2006). [Get PDF] [Supp. Info.] [PubMed link]
Suthram, S., Sittler, T., and Ideker, T. The Plasmodium protein network diverges from those of other eukaryotes. Nature 438(7064):108-12 (2005). [Get PDF] [Supp. Info.] [PubMed link]
Kelley, R. and Ideker, T. Systematic interpretation of genetic interactions using protein networks. Nature Biotechnology 23(5):561-566 (2005). [Get PDF] [PubMed link]
Sharan, R., Suthram, S., Kelley, R. M., Kuhn, T., McCuine, S., Uetz, P., Sittler, T., Karp, R. M., and Ideker, T. Cover Article: Conserved patterns of protein interaction in multiple species. Proc Natl Acad Sci U S A. 8:102(6) 1974-79 (2005). [Get PDF] [PubMed link]
[Suppl. Website and Database of Conserved Pathways]
Ideker, T. Systems biology 101--what you need to know. Nature Biotechnology 22(4): 473-5 (2004). [Get PDF] [PubMed link]
Ideker, T., Thorsson, V., Ranish, J. A., Christmas, R., Buhler, J., Eng, J. K., Bumgarner, R., Goodlett, D. R., Aebersold, R., and Hood, L. Integrated Genomic and Proteomic Analyses of a Systematically Perturbed Metabolic Network. Science, 292: 929-934 (2001). [Get PDF] [Companion Website][Raw Data][PubMed link]